Getting started

MetaSBT is a Python3 framework built for the analysis and characterization of the microbial dark matter. It is available on the Python Package Index as well as Conda on the Bioconda channel and relies on a set of external software dependencies lister in the following sections.

Installing MetaSBT

The pipeline is available for Linux users as a Python 3.8 package that can be install with the following command:

pip install metasbt

MetaSBT is also available as a conda package:

# Make sure you add bioconda to the list of conda channels first
conda config --add channels bioconda
conda config --add channels conda-forge
conda config --set channel_priority strict

# Finally, install MetaSBT
conda install -c bioconda metasbt

MetaSBT can be also installed by simply cloning its repository and running the following commands:

# Clone the MetaSBT repository
mkdir -p ~/git && cd ~/git
git clone https://github.com/cumbof/MetaSBT.git

# Move to the MetaSBT root folder
cd MetaSBT

# Finally install MetaSBT
make install

Congratulations, MetaSBT is now installed in your environment!

Warning

Installing MetaSBT via pip or by cloning its repository is highly discouraged since all the external software dependencies must be installed manually. If you are somehow forced to use these methods, have a look at the list of external software dependencies below and install all of them. Otherwise, please install MetaSBT via conda as explained above.

Tip

You can check whether MetaSBT has been correctly installed by typing the following command in your terminal:

metasbt --version

Dependencies

MetaSBT requires a the following dependencies:

• busco (version >=5.8.3)
• checkm (version >=1.2.4)
• checkv (version >=1.0.3)
• howdesbt (version >=2.00.15)
• kitsune (version >=1.3.5)
• kraken2 (version >=2.1.3)
• ncbitax2lin (version >=2.4.1)
• ntcard (version >=1.2.2)

Warning

MetaSBT makes use of some advanced howdesbt sub-commands that are not available by default when installing HowDeSBT. In order to access advanced commands, HowDeSBT must be install by compiling the software with the alternative version of its Makefile. Note that the required sub-commands are available by default if you install MetaSBT via conda.

For what concerns BUSCO, CheckM2, and CheckV, please remember to install and configure their databases before running MetaSBT. Take a look at their wiki for further instructions.